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- PDB-6p9h: Crystal structure of human anti staphylococcus aureus antibody ST... -

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Basic information

Entry
Database: PDB / ID: 6p9h
TitleCrystal structure of human anti staphylococcus aureus antibody STAU-281 Fab in complex with IsdB NEAT2 domain
Components
  • Human anti staphylococcus aureus antibody STAU-281 Fab heavy chain
  • Human anti staphylococcus aureus antibody STAU-281 Fab light chain
  • Iron-regulated heme-iron binding protein
KeywordsIMMUNE SYSTEM / iron-regulated surface determinant system / IsdB / NEAT2 domain / antibody
Function / homology
Function and homology information


heme transmembrane transporter activity / extracellular region / metal ion binding
Similarity search - Function
Iron-regulated surface determinant protein IsdB / : / Iron-regulated surface determinant protein H/B, linker domain / Immunoglobulin-like - #1850 / NEAT domain / Iron Transport-associated domain / NEAT domain profile. / NEAr Transporter domain / NEAT domain superfamily / : ...Iron-regulated surface determinant protein IsdB / : / Iron-regulated surface determinant protein H/B, linker domain / Immunoglobulin-like - #1850 / NEAT domain / Iron Transport-associated domain / NEAT domain profile. / NEAr Transporter domain / NEAT domain superfamily / : / YSIRK type signal peptide / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / Iron-regulated surface determinant protein B
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.003 Å
AuthorsDong, J. / Crowe, J.E.
CitationJournal: Mbio / Year: 2019
Title: Human V H 1-69 Gene-Encoded Human Monoclonal Antibodies against Staphylococcus aureus IsdB Use at Least Three Distinct Modes of Binding To Inhibit Bacterial Growth and Pathogenesis.
Authors: Bennett, M.R. / Dong, J. / Bombardi, R.G. / Soto, C. / Parrington, H.M. / Nargi, R.S. / Schoeder, C.T. / Nagel, M.B. / Schey, K.L. / Meiler, J. / Skaar, E.P. / Crowe Jr., J.E.
History
DepositionJun 10, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jan 6, 2021Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Iron-regulated heme-iron binding protein
C: Human anti staphylococcus aureus antibody STAU-281 Fab heavy chain
D: Human anti staphylococcus aureus antibody STAU-281 Fab light chain
A: Iron-regulated heme-iron binding protein
H: Human anti staphylococcus aureus antibody STAU-281 Fab heavy chain
L: Human anti staphylococcus aureus antibody STAU-281 Fab light chain


Theoretical massNumber of molelcules
Total (without water)122,0196
Polymers122,0196
Non-polymers00
Water21612
1
B: Iron-regulated heme-iron binding protein
C: Human anti staphylococcus aureus antibody STAU-281 Fab heavy chain
D: Human anti staphylococcus aureus antibody STAU-281 Fab light chain


Theoretical massNumber of molelcules
Total (without water)61,0103
Polymers61,0103
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5280 Å2
ΔGint-33 kcal/mol
Surface area24170 Å2
MethodPISA
2
A: Iron-regulated heme-iron binding protein
H: Human anti staphylococcus aureus antibody STAU-281 Fab heavy chain
L: Human anti staphylococcus aureus antibody STAU-281 Fab light chain


Theoretical massNumber of molelcules
Total (without water)61,0103
Polymers61,0103
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5280 Å2
ΔGint-32 kcal/mol
Surface area24810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.591, 115.296, 88.273
Angle α, β, γ (deg.)90.00, 100.12, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Iron-regulated heme-iron binding protein


Mass: 13896.936 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: isdB, SAMEA1708674_03096 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1D4RDN9, UniProt: Q2FZF0*PLUS
#2: Antibody Human anti staphylococcus aureus antibody STAU-281 Fab heavy chain


Mass: 23915.807 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody Human anti staphylococcus aureus antibody STAU-281 Fab light chain


Mass: 23196.803 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.98 Å3/Da / Density % sol: 58.73 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium citrate tribasic, pH 5.5, 16% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Oct 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 3→48.04 Å / Num. obs: 28660 / % possible obs: 99.8 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 15.2
Reflection shellResolution: 3→3.16 Å / Rmerge(I) obs: 0.316 / Num. unique obs: 4141

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Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RTL

3rtl


Resolution: 3.003→48.039 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.19
RfactorNum. reflection% reflection
Rfree0.225 1325 4.63 %
Rwork0.2064 --
obs0.2073 28630 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.003→48.039 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8154 0 0 12 8166
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0028327
X-RAY DIFFRACTIONf_angle_d0.51911326
X-RAY DIFFRACTIONf_dihedral_angle_d10.4574959
X-RAY DIFFRACTIONf_chiral_restr0.0431286
X-RAY DIFFRACTIONf_plane_restr0.0041462
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0025-3.12270.34721340.3092985X-RAY DIFFRACTION99
3.1227-3.26480.33211430.2753032X-RAY DIFFRACTION100
3.2648-3.43690.30961310.25133043X-RAY DIFFRACTION100
3.4369-3.65220.2461530.23043018X-RAY DIFFRACTION100
3.6522-3.9340.24261450.21853019X-RAY DIFFRACTION100
3.934-4.32970.20461390.18633051X-RAY DIFFRACTION100
4.3297-4.95570.1691630.16093041X-RAY DIFFRACTION100
4.9557-6.24150.20991660.18433027X-RAY DIFFRACTION100
6.2415-48.04480.19491510.1913089X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 27.5803 Å / Origin y: 9.7445 Å / Origin z: -15.1242 Å
111213212223313233
T0.3736 Å2-0.0149 Å20.0084 Å2-0.2679 Å20.0659 Å2--0.3321 Å2
L0.7362 °2-0.2199 °20.0027 °2-0.354 °20.1855 °2--0.4433 °2
S-0.0215 Å °0.0427 Å °-0.0372 Å °0.0171 Å °-0.0009 Å °0.022 Å °-0.0323 Å °0.0887 Å °0.0144 Å °
Refinement TLS groupSelection details: all

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